SACRAMENTO — Gov. Gavin Newsom’s assertion that shipments of medical masks the state bought from a Chinese manufacturer had simply been delayed because of federal safety certification issues was thrown into doubt Wednesday when regulators said they had actually rejected the masks.

Many of the N95 particulate-filtering respirators California planned to buy from supplier BYD in a $1 billion deal are now in limbo while the company tries to secure safety certification.

Katie Shahan, a spokeswoman for the National Institute for Occupational Safety and Health, said the agency had denied safety certification of the masks “based on a number of factors.” She said federal rules prohibit the agency from disclosing the specific reasons.

“NIOSH tested the received hardware; however, the review of the documentation provided to NIOSH for the design, manufacturing and quality inspection of the device was concerning,” Shahan wrote in an email.

Last week, Newsom told reporters that federal certification of the masks had been delayed. He said he was optimistic the deal would move forward soon.

“The unfortunate news, but it’s part of these larger contracts, is on the back end we needed some certification, federal certifications, for these N95 respirator masks,” Newsom said at a news conference May 6.

“That’s been delayed a little bit, so on the back end, a little bit of delay,” he said.

Brian Ferguson, a spokesman for the Governor’s Office of Emergency Services, stressed that if BYD doesn’t obtain certification, the state will receive its money back under the contract. Newsom’s administration did not address his prior comment on “delayed” certification.

“We remain optimistic that the vendor will meet its obligations,” Ferguson wrote in an email. “Should the contractor fail to meet that high standard, we have built in strong provisions to protect the state.”

The situation led California to seek repayment of half the $495 million that it paid upfront to BYD for N95 particulate-filtering respirators intended to protect medical workers on the front lines of the coronavirus pandemic.

Under its contract with California, BYD was supposed to obtain safety certification for the N95 masks by April 30. California has renegotiated part of the contract to give the company until May 31. If BYD cannot obtain certification, the company must refund the other half of the state’s $495 million prepayment.

BYD had agreed to supply 300 million of the N95 masks. It also is sending 100 million lower-grade surgical masks to California as part of the $1 billion deal. The federal government does not need to certify those masks, and more than 18 million have already been delivered.

BYD spokesman Frank Girardot said the federal agency had denied safety certification for the N95 masks because of “a “documentation control” issue, and said the quality of the masks was not the problem. He said the company is still hopeful it can receive certification by the end of the month.

“Our masks have passed the most important part of the test,” Girardot said. “We’re working with (federal regulators) on a corrective action plan, to have the documentation control that NIOSH expects.”

He suggested the company has been treated unfairly and received extra scrutiny in the U.S. media because it is based in China.